The MSR Conspiracy
by mfluderX
Summary: the Smoking Man has other plans for Mulder and Scully.The whole series from a new angle,MSR please R R
1. before they met

The MSR Conspiracy

Summary:the Smoking Man has other plans for Mulder and Scully. The whole series from a new angle,MSR please R+R

Disclaimer: You know the drill, I don't own Mulder, Scully, X-Files, or anything but some X-Files merchandise-ok- a lot of X-Files merchandise.

Chris Carter owns them. But don't think I wouldn't take them if offered.

And please don't sue me, as all you will get is a modest X-Files collection -ok- a not-so-modest X-Files collection, which I am sure you already have.

Chapter 1(before they met)

Diana Fowley screwed up. Big time. She was supposed to get Fox Mulder to trust her-while keeping an eye on him. And she had, she had helped Mulder open the X-Files by introducing him to Senator Richard Matheson (who was a crony of her Boss-her real boss, not the people she worked for at the F.B.I. She was only there to serve her boss's agenda). She became his partner, helping him in his quest for the Truth (and cleverly impeding him when he got too close). She became his lover (her boss wanted it for some reason-but he would never tell her). Diana had been keeping close watch on Mulder for over a year now, and Mulder had the X-Files for 3 months now (her boss wanted Mulder to have them for some reason,but Mulder had to believe that he was forever on the edge of losing the section).

And Fowley did her job perfectly, until she really did fall in love with Fox Mulder.

Recently, Mulder had found proof of the existence of extraterrestrial life, and They had to make the evidence disappear. Mulder was gettingclose-too close to the Truth, and Fowley could have stopped him. Diana Fowley was becoming a liability.

She was to break it off with Mulder, or else.

By the time she had accepted the assignment overseas; Mulder was not surprised.

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46th ST New York City February 10th 10:31pm

"Is he here?" Ethan Minette asked the butler as he walked through the front door.

"Yes." Answered the butler, who then showed him into a small paneled room that smelled of stale cigarette smoke. The butler gestured to a black leather chair in the middle of the room, "Please have a seat, he will be with you in a moment."

A moment after the butler left, the Cigarette-Smoking Man walked in, sat down, and said, "Who do you have in mind?"

Ethan handed CSM a file an inch thick. "Her name is Dana Scully, she's a doctor who currently teaches at Quantico."

"A doctor?" CSM asked.

"With her qualifications, she won"t object to the assignment."

Flipping through the file, CSM stopped at a page, read it ,and said, "This says that she"s by-the-book. How are we going to get her to ignore her orders?"

"Scully's a fair woman. She will give herself time to figure out Mulder and to make her own opinions about him. She will see what we want her to see."

"How do you know for sure?"

"I figured the best way to learn as much as I can about her without her becoming suspicious was to become her boyfriend." An evil little grin crossedhis face. "A feat, as Scully really doesn't want a boyfriend, she just doesn't want to be alone, if you know what I mean."

"When Scully's had time to get to know Mulder and has softened up to him a little, we start showing her what he suffers for his beliefs.We makeMulder a St. Sebastian in her eyes. Scully's a Catholic, she'll fall for it." Ehtan gave a little laugh and continued, "And then,I'll give her an ultimatum, either she debunks the X-Files and sends Mulder back to VICAP or I'll leave her."

"How do you know that she'll choose to break up with you?"CSM asked with a frown, he did not like changes in his plans.

"Our 'affair' is cooling off. And Scully will not tolerate an ultimatum,she'll dump me faster than you can say 'conspiracy', and will stick to Mulder for the simple fact that she wants to be around someone who can respect her opinion."

CSM was impressed,the Plan just might work. "One more thing."

"Yes?"

"Is she a match for the Program?"

"If we time it perfectly, we can not only place the Colonist's DNA in her system,but we can also bring them closer together-play on Samantha'sabduction,and give Scully another reason to follow Mulder. After Scully's abduction, We leave them alone,and let the Group work on their plans,Mulder and Scully will finish our plans for us.But it's going to take time."

"The rewards will be worth the wait," said CSM," by this time next month, the Plan will be in motion. You did well,Ethan." That was Ethan's dismissal, but he stayed.

"Is there something else,Ethan?"

"I was wondering,Fowley was to keep Mulder from the Truth, Scully's there to help him. How do we hide things now?"

"The same way we kept it from him when Fowley disregarded her orders," said CSM," They will take care of it."

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	2. the meeting

yes i know that you all know this part already,but I can't do the story right without it.

Chapter 2 The meeting

March 6th, 1992

As Dana Scully stepped onto the 5th floor of the headquarters of the Federal Bureau of Investigation, she checked the note the agent had interrupted her class that morning to give her.

"Your attendance is required at the FBI headquarters at 1600 hours sharp. 5th floor."

She walked to the receptionist's desk and flashed her badge, "I have a meeting with…."

"Agent Scully?"

"Yes"

"Follow me."

Scully was shown down a windowless hallway with a door at the end of it. She knocked on the door and it was opened.

Scully received an appreciating nod from the man who opened the door. He was in his 50s-and holding a cigarette.

"_What happened to no smoking in government buildings," _Scully thought. Something about this man made her instantly dislike him.

The man seated behind the desk was Scott Blevins. "Agent Scully, thank you for coming on such short notice. Please... "He motions for her to sit down. "We see you've been with us just over two years."

" Yes, sir."

" You went to medical school but you chose not to practice. How'd you come to work for the F.B.I.?"

" Well, sir, I was recruited out of medical school. Um, my parents still think it was an act of rebellion, but, uh... I saw the F.B.I. as a place where I could distinguish myself."

Another man in the room asked: "Are you familiar with an agent named Fox Mulder?"

"Yes, I am."

Blevins asked: "How so?"

"By reputation. He's an Oxford educated Psychologist, who wrote a monograph on serial killers and the occult, that helped to catch Monty Props in 1988. Generally thought of as the best analyst in the violent crimes section. He had a nickname at the academy... Spooky Mulder." She smiles at the Cigarette-Smoking Man, who gives no response.

"What I'll also tell you is that Agent Mulder has developed a consuming devotion to an unassigned project outside the bureau mainstream. Are you familiar with the so-called "X-Files?"

"I believe they have to do with unexplained phenomena."

"More or less. The reason you're here, Agent Scully, is we want you to assist Mulder on these X-Files. You will write field reports on your activities, along with your observations on the validity of the work."

"Am I to understand that you want me to debunk the X-Files project, sir?"

"Agent Scully, we trust you'll make the proper scientific analysis. You'll want to contact Agent Mulder shortly. We look forward to seeing your reports."

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The Basement 4:45 pm

Scully had no idea what to expect-which was good, because she wanted to make up her own mind. At the bottom of the stairs, Scully found a door marked, "Fox Mulder, Special Agent." She knocked.

"Sorry, nobody down here but the FBI's most unwanted," said a voice from the other side of the door. Scully opened the door and entered the office.

It was like no other office on the FBI. Books lined one wall from floor to ceiling. Tables were piled high with stacks of papers and reports. There were more on the floor. The walls were covered with photos of blurry objects. There was a wall poster that said, "I WANT TO BELIEVE." And though the room looked chaotic at first glance, Scully could tell that Mulder could find anything in it at a glance.

Mulder was sitting at a table when she entered. He was examining a photo slide under an intense light. He put the slide in the projector. And he turned around.

Scully got her first good look at him, even then it was hard to get a fix on him. It was like trying to put together two parts of a puzzle that didn't seem to fit. His face was young for an FBI agent. His hair was longer than most. And she could tell that he wore his glasses as little as possible.

And his eyes.

There was something old and haunted in his eyes, something knowing, something wise.

"Agent Mulder. I'm Dana Scully, I've been assigned to work with you."

He shakes her hand and says, " Oh, isn't it nice to be suddenly so highly regarded? So, who did you tick off to get stuck with this detail, Scully?"

"Actually, I'm looking forward to working with you. I've heard a lot about you."

"Oh, really? I was under the impression... that you were sent to spy on me, "he says with a smile.

"If you have any doubt about my qualifications or credentials, th..."

Mulder stands and takes out a paper from a pile with his telephone as a paperweight. "You're a medical doctor, you teach at the academy. You did your undergraduate degree in physics." He takes off his glasses and looks at the paper. "Einstein's Twin Paradox, A New Interpretation. Dana Scully Senior Thesis." Now that's a credential, rewriting Einstein.

"Did you bother to read it?"

"I did. I liked it. It's just that in most of my work, the laws of physics rarely seem to apply." He walks past her and turns off the lights. She glares at him slightly. "Maybe I can get your medical opinion on this, though." Mulder turns on the projector. On it there is a woman dead. "Oregon female, age twenty-one, no explainable cause of death. Autopsy shows nothing. Zip." He changes the slide to that of the two bumps on her back. " There are, however, these two distinct marks on her lower back. Doctor Scully, can you ID these marks?"

"Needle punctures, maybe. An animal bite. Electrocution of some kind." She walks up to the view screen. He changes the slide to that of a molecular diagram.

"How's your chemistry? This is the substance found in the surrounding tissue."

"It's organic. I don't know, is it some kind of synthetic protein?"

"Beats me, I've never seen it before either. "The next slide is of a boy facedown on railroad tracks, his shirt lifted in the back. "But here it is again in Sturgis, South Dakota." The final slide if of a close-up of another set of bumps. "And again in Shamrock, Texas."

" Do you have a theory?"

"I have plenty of theories." He walks over to her and says, "Maybe what you can explain to me is why it's bureau policy to label these cases as 'unexplained phenomenon' and ignore them. Do you believe in the existence of extraterrestrials?" He whispers the last few words eerily and she smiles.

"Logically, I would have to say "no." He nods, having expected that answer. "Given the distances needed to travel from the far reaches of space, the energy requirements would exceed a spacecraft's capabilities th..."

"Conventional wisdom. You know this Oregon female? She's the fourth person in her graduating class to die under mysterious circumstances. Now, when convention and science offer us no answers, might we not finally turn to the fantastic as a plausibility?"

"The girl obviously died of something. If it was natural causes, it's plausible that there was something missed in the post-mortem. If she was murdered, it's plausible there was a sloppy investigation. What I find fantastic is any notion that there are answers beyond the realm of science. The answers are there. You just have to know where to look."

"That's why they put the 'I' in 'F.B.I.' See you tomorrow morning, Scully, bright and early." He walks back over to his desk and sits down. "We leave for the very plausible state of Oregon at eight A.M." She smiles and walks out.

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Upstairs, the smoking man sat in an empty boardroom and listened to their conversation. He had a pair of headphones on. He smiled. This was going to be interesting.

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	3. the St Sebastian Setup

Chapter 3: The St. Sebastian setup

July

Scully was having lunch with Tom Colton, a friend who attended Quantico with her. He was telling her about a case he had. Three murders began six weeks ago; victims vary in age, race, gender, and no known connections to each other. Only connection was the lack of Point of entry. Each victim was found with his or her liver, ripped out. No cutting tools used.

Colton kept peppering the conversation with comments like, "Have you had any close encounters of the third kind?" and, "Spooky Mulder."

Colton left the discussion with, "And you, maybe you won't have to be Mrs. Spooky anymore."

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The next morning, when Scully and Mulder met Colton, the first thing Colton said was, "So, Mulder, what do you think, does this look like the work of little green men?"

"Grey."

"Excuse me."

"Grey. You said green men, a Reticulan skin tone is actually gray, and they're notorious for their extraction of terrestrial human livers. Due to iron depletion in the Reticulan galaxy."

"You can't be serious."

"Do you have any idea what liver and onions go for on Reticula?"

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The next morning, Scully gave a report to VCS, "…victim. When this occurs, a serial killer may, return in  
frustration to the sight of a previous murder, hoping to, recapture the emotional high. I think our best course of action is to target these sights." She finished her report.

"Good job, Agent Scully. If there are no objections, I'd like to begin our stakeouts of the murder sites tonight. We're looking for a male, twenty-five to thirty-five, possibly wearing a uniform, gas company, UPS, whatever. I know you're assigned to another area Scully, but if you don't mind some overtime, you're welcome to come aboard with us, on this. Erm, that is if you don't mind working in an area that's a bit more down-to-earth." The other agent in the office chuckled at that.

"_Is this how Mulder is always treated?"_ Scully wondered. She forced a smile, but she was not amused.

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Three days later

They had caught a suspect, Eugene Victor Tooms. He was found in an air duct of the building that had been the site of the most recent murder.

Tooms was being questioned with a lie detector. Every now and then, there was a question that was…. weird, ""Are you over one hundred years old?"" Have you ever been to Pal Hatton Mill?","In 1933?" This was making Colton furious.

After the interrogation, Colton was treating Mulder like a dog that had rolled in something smelly and dragged it all over the house. And Mulder was acting like a nut-on purpose.

Scully had to make a choice, either work with Colton and VCS-a position any agent would be envois of, or stay with Mulder.

She took Mulder aside and asked, "Why did you do that?"

"Do what?"

"You knew they wouldn't believe you, why did you push it?"

"Maybe I thought you caught the right guy."

"And?"

"Okay, and maybe I run into so many people, who are hostile, just because they can't open their minds to the… possibilities, that sometimes the need to mess with their heads outweighs the millstone of humiliation."

"It seems like you were acting very territorial, I don't know, forget it."

"Of course I was, in our investigations, you may not always agree with me but at least you respect the journey. And if you want to continue working with them, I won't hold it against you."

With that, Scully made her decision.

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A few days later, Colton met with Ethan Minette.

"…after the polygraph, she decided to work with Mulder. And when she made that choice, I started doing everything I could to get Mulder fired-like you told me to."

"What did Scully do?"

"Everything! I've got a month's suspension without pay!" Colton was angry, "And it's all because of you!"

"Tom, calm down. Everything worked out just like I wanted it to."

"You wanted me to nearly get fired!"

"No, that's just a consequence; I have already taken the necessary steps to set your record right. By the end of your suspension, your record will be clean and you will be on the fast track again. No worries." Ethan then handed Colton $3000 and said, "Will that be enough?"

"How are you able to change my record?"

"There are many ways, my friend, many ways." Something in this chilled Colton to the bone.

When Colton left, Ethan pulled out a cell phone and dialed a number. "She fell for it," he said.

"Good, now finish it," the voice of the Cigarette-Smoking Man answered on the other end.

Ethan hung up and said, "Show time."

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One week later, Scully had a date with Ethan. It had been a while since they had seen each other, as they both kept canceling because of work.

A knock on the door startled Scully. Ethan was early.

"Hey, long time, no see," said Ethan as he entered and promptly plopped down on the couch. "I heard about your fight with Tom Colton."

"And?"

"I thought you would've debunked Spooky by now."

At this, Scully eyed him coldly, the memory of last week still fresh in her mind. "Don't call Mulder that, Ethan, I won't tolerate it," she said, and then added, "And I'm not going to debunk him."

"Why not, the guy's a nut!"

The room had a chill that had nothing to do with the temperature.

"Mulder's not crazy."

"So you're just going to ignore your orders?"

"My orders were to observe the validity of Mulder's work and write reports. That's all."

"So what do you write in your reports, Dana?" Ethan said with mock interest.

"I write that Mulder's brilliant, that-"

"That he's brainwashed you?" Ethan interrupted.

"You're being ridiculous."

"Why not ditch 'Spooky' and go back to teaching. Send Mulder back to VICAP, and get that promotion you were promised back in march. Save yourself!"

"I've seen things, Ethan," Scully said as though she pitied Ethan.

"You know what Dana,"Ethan said angrily, "I've heard they call you Mrs. Spooky now and-"

"Get out."

"What?"

"You heard me, get out, I can't be with anyone who won't respect me enough to respect my decisions." Ethan left.

Throughout it all, Scully never raised her voice. She had expected this to happen sooner or later. And he was CIA, it was his job to know these things. And, she realized, she wouldn't miss him at all.

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When Ethan left the apartment, he grinned, "mission accomplished."

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	4. abduction and return

sorry it took so long, i've been writing chapter 5 and forgot to type up this chapter i promise chapter 5 is much better

Chapter 4 abduction/return

September: their second year

The X-Files was closed-had been for some time. But Scully helped Mulder as often as possible.

Mulder was getting a new partner, Alex Krycek. The kid practically fawns over Mulder. Scully expected him to ask for an autograph any day now. Krycek never questioned, and he never disagreed.

Mulder and Krycek were talking one day when Scully came up and Krycek left.

"Oh look, Scully, you ran off my fan club."

"Must be nice, not having someone questioning your every move, poking holes in all your theories," Scully teased.

"Oh yeah…yeah it's great. I'm surprised I put up with you for so long."

Krycek returned. In a moment he had Mulder and Scully recounting cases they had worked together

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After Krycek's first assignment with Mulder, Krycek met with CSM, Krycek was giving a report, "Reassigning them to other areas seems to have only strengthened their determination. Scully's a problem. A much larger problem than you described."

"Every problem has a solution."

After Krycek left, Ethan walked in and asked, "What does he know?"

"Don't worry, Ethan, he only knows what the group wants of Mulder and Scully, he knows nothing of our plans. Do you think believe that it's time?"

"Yes."

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October

Scully was gone, and the guy that killed her was dead, killed by Alex Krycek. The only thing they found of her at the abduction site

The X-Files had been reopened. Skinner believed that that was the thing that those who took Scully would fear the most.

No one could find Scully.

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Until today.

She turned up in a hospital. No one knew when, or how, she got there. There were no admissions forms. Mulder was pissed. At one point, Mulder had to be taken away by two security guards who were barely able to pull Mulder away because Mulder was pulling so hard to get at the doctor he believed had something to do with what happened to Scully.

Scully was an inch from death. Her mother had taken her off life support. Mulder fought against it, he believed that Scully could survive and that no one was giving her the chance to do so. Scully survived.

Days later, Scully opened her eyes. When Mulder got the call, he rushed straight to the hospital.

"I had the strength of your beliefs," Scully said as though she knew that Mulder fought for her while she was in her coma. Mulder gave her the cross which was the only thing they found of her at the abduction site.

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